[gmx-developers] Modification of calculation of the force

Camilo Andrés Jimenez Cruz camilo.jimenezc at gmail.com
Wed Aug 12 17:17:21 CEST 2009

Ups, I found what I was looking for in the README.

nb010_sse (No Coul, VdW=Lennard-Jones, no water optimization)
nb030_sse (No Coul, VdW=Table, no water optimization)
nb100_sse (Coul=Normal, No VdW, no water optimization)
nb101_sse (Coul=Normal, No VdW, water=SPC/TIP3P-other atom)
nb102_sse (Coul=Normal, No VdW, water=SPC/TIP3P-SPC/TIP3P)
nb103_sse (Coul=Normal, No VdW, water=TIP4P-other atom)
nb104_sse (Coul=Normal, No VdW, water=TIP4P-TIP4P)
nb111_sse (Coul=Normal, VdW=L-J, water=SPC/TIP3P-other atom)
nb112_sse (Coul=Normal, VdW=L-J, water=SPC/TIP3P-SPC/TIP3P)
nb113_sse (Coul=Normal, VdW=L-J, water=TIP4P-other atom)
nb114_sse (Coul=Normal, VdW=L-J, water=TIP4P-TIP4P)
nb201_sse (Coul=RF, No VdW, water=SPC/TIP3P-other atom)
nb202_sse (Coul=RF, No VdW, water=SPC/TIP3P-SPC/TIP3P)
nb203_sse (Coul=RF, No VdW, water=TIP4P-other atom)
nb204_sse (Coul=RF, No VdW, water=TIP4P-TIP4P)
nb211_sse (Coul=RF, VdW=L-J, water=SPC/TIP3P-other atom)
nb212_sse (Coul=RF, VdW=L-J, water=SPC/TIP3P-SPC/TIP3P)
nb213_sse (Coul=RF, VdW=L-J, water=TIP4P-other atom)
nb214_sse (Coul=RF, VdW=L-J, water=TIP4P-TIP4P)
nb301_sse (Coul=Table, No VdW, water=SPC/TIP3P-other atom)
nb302_sse (Coul=Table, No VdW, water=SPC/TIP3P-SPC/TIP3P)
nb303_sse (Coul=Table, No VdW, water=TIP4P-other atom)
nb304_sse (Coul=Table, No VdW, water=TIP4P-TIP4P)
nb311_sse (Coul=Table, VdW=L-J, water=SPC/TIP3P-other atom)
nb312_sse (Coul=Table, VdW=L-J, water=SPC/TIP3P-SPC/TIP3P)
nb313_sse (Coul=Table, VdW=L-J, water=TIP4P-other atom)
nb314_sse (Coul=Table, VdW=L-J, water=TIP4P-TIP4P)
nb331_sse (Coul=Table, VdW=Table, water=SPC/TIP3P-other atom)
nb332_sse (Coul=Table, VdW=Table, water=SPC/TIP3P-SPC/TIP3P)
nb333_sse (Coul=Table, VdW=Table, water=TIP4P-other atom)
nb334_sse (Coul=Table, VdW=Table, water=TIP4P-TIP4P)

2009/8/12 Camilo Andrés Jimenez Cruz <camilo.jimenezc at gmail.com>:
> Hi!
> Pieter, thanks for the hint.  I tried simulating a box with just TIP3P
> water by using this option, but the results I get for energy  and
> structure (rdf) are very different to the ones I get without this
> option. Is there something I am missing out?
> By the way, I am required now to implement the changes in gromacs
> v3.3.3, so I am looking at the code in gmxlib/nonbonded/nonbonded.c.
> So far, I get that, the function to change is the one pointed by
> kernelptr, and that those functions are written in assembler for each
> architecture. But I haven't been able to find which one of the
> assembler codes for my architecture
> (/data/gaia-disk05/jimenc/AcceleratedMolecularDynamics/local/gromacs/src/gromacs-3.3.3/src/gmxlib/nonbonded/nb_kernel_x86_64_sse)
> is the one being executed. Is there an easy way to find this out?
> Thanks in advance!
> On Sun, Aug 9, 2009 at 4:21 AM, Pieter van 't
> Hof<pieter.van.t.hof at logica.com> wrote:
>> Hi,
>> In Gromacs 4 you can set the environment variable GMX_NB_GENERIC (using
>> in bash:$ export GMX_NB_GENERIC=1)
>> Then plain C loops in src/gmxlib/nonbonded/nb_generic.c will be used.
>> This is where the forces per atom are calculated. From there on you can
>> implement the function you want.
>> On Sat, 2009-08-08 at 17:22 -0400, Camilo Andrés Jimenez Cruz wrote:
>>> Hi everybody.
>>> I would like your advise in modifying the source code of gromacs, in
>>> such a way that the force is calculated by using a modified potential
>>> that goes like V' = V + function(V), where function(V) is a simple
>>> function of V (or Force = Force + function(Force)).
>>> I just started checking the code, but I thought your help could save
>>> me many days.
>>> I am using gromacs-4.0.5, but I don't have a requirement to stick to
>>> this version.
>>> Thanks in advance!
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> --
> Camilo Andrés Jiménez Cruz

Camilo Andrés Jiménez Cruz

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